Objective: We reported a high incidence of thrombosis, central pulmonary artery hypoplasia, and mortality for bilateral bidirectional cavopulmonary shunts. We hypothesized that technical modifications in the cavopulmonary anastomosis and anticoagulation would limit thrombus and central pulmonary artery hypoplasia, and thereby improve outcomes. Methods: Sixty-one patients (median age, 8.4 months; weight, 6.6 kg) underwent bilateral bidirectional cavopulmonary shunt from 1990 to 2007. The cohort was divided into 2 groups: 1) the conventional group (1990-1999, n = 37) and 2) the V-shaped group, with a hemi-Fontan or modification in which the cavae were anastomosed to the pulmonary artery adjacent to each other so they formed the appearance of a V (1999-2007, n = 24). Central and branch pulmonary artery growth, survival, and reinterventions were determined. Results: The pre-Fontan study showed equivalent superior venae cavae and Nakata indices. The central pulmonary artery index and central pulmonary artery/Nakata index ratio were significantly higher in the V-shaped group (P < .05). There were no differences in freedom from death or transplant (conventional 69% vs V-shaped 75% at 3 years, P = .5), and a nonsignificant trend toward improving freedom from reinterventions (63% vs 81% at 3 years, P = .15) and thrombosis (82% vs 95% at 1 year, P = .11) was observed in the V-shaped group. Multivariate analysis showed anastomotic strategy, low saturation, and thrombosis were predictors for death. Anastomotic strategy, lack of anticoagulation, thrombosis, and small superior venae cavae were predictors for reintervention (P < .05). Predictors for thrombus included small superior venae cavae, Nakata index, and low saturation (P < .03). Conclusions: Surgical modifications for bilateral bidirectional cavopulmonary shunts were associated with the larger central pulmonary artery size. Lack of anticoagulation and anastomotic strategy affected reintervention. Anastomotic strategy and postoperative thrombus affected mortality. © 2010 by The American Association for Thoracic Surgery.